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A 2.57-Approximation Algorithm for Contig-Based Genomic Scaffold Filling

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Algorithmic Aspects in Information and Management (AAIM 2019)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11640))

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Abstract

Genomic Scaffold Filling problem forms an important class of problems, and has been paid lots of attention in the literature. In this paper, we study one of the Genomic Scaffold Filling problem, called One-sided-GSF-max-BC problem. The previous approximation ratio for the problem is 2. However, as we pointed out in the introduction part, the ratio 2 algorithm in the literature can only deal with special instances of the problem, not really solve the One-sided-GSF-max-BC problem. In this paper, we give an approximation algorithm of ratio 2.57 for the One-sided-GSF-max-BC problem. Our method is based on auxiliary graphs constructed and two applications of finding maximum matching in auxiliary graphs.

This work is supported by the National Natural Science Foundation of China under Grants (61672536, 61420106009, 61872450, 61828205), Hunan Provincial Science and Technology Program (2018WK4001).

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Authors and Affiliations

  1. School of Information Science and Engineering, Central South University, Changsha, 410083, People’s Republic of China

    Qilong Feng, Xiangzhong Meng, Guanlan Tan & Jianxin Wang

Authors
  1. Qilong Feng
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  2. Xiangzhong Meng
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  3. Guanlan Tan
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  4. Jianxin Wang
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Corresponding author

Correspondence to Qilong Feng .

Editor information

Editors and Affiliations

  1. The University of Texas at Dallas, Richardson, TX, USA

    Ding-Zhu Du

  2. Hefei University of Technology, Hefei, China

    Lian Li

  3. Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

    Xiaoming Sun

  4. Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

    Jialin Zhang

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Feng, Q., Meng, X., Tan, G., Wang, J. (2019). A 2.57-Approximation Algorithm for Contig-Based Genomic Scaffold Filling. In: Du, DZ., Li, L., Sun, X., Zhang, J. (eds) Algorithmic Aspects in Information and Management. AAIM 2019. Lecture Notes in Computer Science(), vol 11640. Springer, Cham. https://doi.org/10.1007/978-3-030-27195-4_9

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  • DOI: https://doi.org/10.1007/978-3-030-27195-4_9

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-27194-7

  • Online ISBN: 978-3-030-27195-4

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